MultiMap: a tool to automatically extract and analyse spatial microscopic data from large stacks of confocal microscopy images

Varando, Gherardo and Benavides Piccione, Ruth and Muñoz Cespedes, Alberto and Kastanauskaite, Asta and Bielza Lozoya, María Concepción and Larrañaga Múgica, Pedro María and De Felipe Oroquieta, Javier (2018). MultiMap: a tool to automatically extract and analyse spatial microscopic data from large stacks of confocal microscopy images. "Frontiers in Neuroanatomy", v. 12 ; pp. 1-12. ISSN 1662-5129. https://doi.org/10.3389/fnana.2018.00037.

Description

Title: MultiMap: a tool to automatically extract and analyse spatial microscopic data from large stacks of confocal microscopy images
Author/s:
  • Varando, Gherardo
  • Benavides Piccione, Ruth
  • Muñoz Cespedes, Alberto
  • Kastanauskaite, Asta
  • Bielza Lozoya, María Concepción
  • Larrañaga Múgica, Pedro María
  • De Felipe Oroquieta, Javier
Item Type: Article
Título de Revista/Publicación: Frontiers in Neuroanatomy
Date: May 2018
ISSN: 1662-5129
Volume: 12
Subjects:
Freetext Keywords: Segmentation; Object detection; Fluorescent image; Puncta segmentation; Vglut1; Vgat; Brain atlas; ImageJ
Faculty: E.T.S. de Ingenieros Informáticos (UPM)
Department: Inteligencia Artificial
Creative Commons Licenses: Recognition - No derivative works - Non commercial

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Abstract

The development of 3D visualization and reconstruction methods to analyse microscopic structures at different levels of resolutions is of great importance to define brain microorganization and connectivity. MultiMap is a new tool that allows the visualization, 3D segmentation and quantification of fluorescent structures selectively in the neuropil from large stacks of confocal microscopy images. The major contribution of this tool is the posibility to easily navigate and create regions of interest of any shape and size within a large brain area that will be automatically 3D segmented and quantified to determine the density of puncta in the neuropil. As a proof of concept, we focused on the analysis of glutamatergic and GABAergic presynaptic axon terminals in the mouse hippocampal region to demonstrate its use as a tool to provide putative excitatory and inhibitory synaptic maps. The segmentation and quantification method has been validated over expert labeled images of the mouse hippocampus and over two benchmark datasets, obtaining comparable results to the expert detections.

Funding Projects

TypeCodeAcronymLeaderTitle
Government of SpainC080020-09UnspecifiedUnspecifiedCajal Blue Brain Project
Government of SpainTIN2016-79684-PUnspecifiedUniversidad Politécnica de MadridAvances en clasificación multidimensional y detección de anomalías con redes bayesianas
Horizon 2020785907HBP SGA2UnspecifiedHuman Brain Project Specific Grant Agreement 2
Madrid Regional GovernmentS2013/ICE-2845CASI – CAMUnspecifiedConceptos y aplicaciones de los sistemas inteligentes

More information

Item ID: 54546
DC Identifier: http://oa.upm.es/54546/
OAI Identifier: oai:oa.upm.es:54546
DOI: 10.3389/fnana.2018.00037
Official URL: https://www.frontiersin.org/articles/10.3389/fnana.2018.00037/full
Deposited by: Memoria Investigacion
Deposited on: 16 May 2019 07:24
Last Modified: 16 May 2019 07:24
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